13C-MFA is far from being a simple assay for quantifying metabolic activity. It requires considerable up-front experimental planning and familiarity with the cell culture system in question, as well as optimized analytics and adequate computation frameworks. The success of a 13C-MFA experiment is ultimately rated by the ability to accurately quantify the flux of one or more reactions of interest. In this chapter, we describe the different 13C-MFA strategies that have been developed for the various fermentation or cell culture systems, as well as the limitations of the respective strategies. The strategies are affected by many factors and the 13C-MFA modeling and experimental strategy must be tailored to conditions. The prevailing philosophy in the computation process is that any metabolic processes that produce significant systematic bias in the labeling pattern of the metabolites being measured must be described in the model. It is equally important to plan a labeling strategy by analytical screening or by heuristics.